PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, transcription initiation factor TFIID 140 kDa subunit (TAF140), or TAFII-140, is an integral component of TFIID) is a general initiation factor (GTF) that plays a key role in preinitiation complex (PIC) assembly through core promoter recognition. The interaction of H3K4me3 with TAF3 directs global TFIID recruitment to active genes, which regulates gene-selective functions of p53 in response to genotoxic stress. TAF3 is highly enriched in embryonic stem cells and is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. Moreover, TAF3, along with TRF3, forms a complex that is essential for myogenic differentiation. TAF3 contains a plant homeodomain (PHD) finger. This family also includes Drosophila melanogaster BIP2 (Bric-a-brac interacting protein 2) protein, which functions as an interacting partner of D. melanogaster p53 (Dmp53).

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 405113028 867 ICPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKC 912
Cdd:cd15522    1 ICPICKKPDDGSPMIGCDECDDWYHWECVGITDEPPEEDDWFCPKC 46

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 405113028  235 DSTDLAPPSPEPPMLAPFAKSQLPIAKPLETKPFTP-KTKTKASSPGQKTKSPKAALSPARLGSPIRSPKTIPKEKKSPG 313
Cdd:pfam05109 426 ESTTTSPTLNTTGFAAPNTTTGLPSSTHVPTNLTAPaSTGPTVSTADVTSPTPAGTTSGASPVTPSPSPRDNGTESKAPD 505

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 405113028  314 RSKSPKSPKSPKIVTHVPQPPVRPETPNRT--------PSAMVVEKTVKETIPVKPTQTP-PETGKLNIEMQLKKGVVTD 384
Cdd:pfam05109 506 MTSPTSAVTTPTPNATSPTPAVTTPTPNATsptlgktsPTSAVTTPTPNATSPTPAVTTPtPNATIPTLGKTSPTSAVTT 585

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 405113028  385 KTIDDSIDAViaracAEREP--DPFEFSSGSESEGDTFTSPKRISVSECTTPKASTSSNNFTKSLATPLPLSG--GTSSS 460
Cdd:pfam05109 586 PTPNATSPTV-----GETSPqaNTTNHTLGGTSSTPVVTSPPKNATSAVTTGQHNITSSSTSSMSLRPSSISEtlSPSTS 660

                  ...
gi 405113028  461 DNS 463
Cdd:pfam05109 661 DNS 663

PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, transcription initiation factor TFIID 140 kDa subunit (TAF140), or TAFII-140, is an integral component of TFIID) is a general initiation factor (GTF) that plays a key role in preinitiation complex (PIC) assembly through core promoter recognition. The interaction of H3K4me3 with TAF3 directs global TFIID recruitment to active genes, which regulates gene-selective functions of p53 in response to genotoxic stress. TAF3 is highly enriched in embryonic stem cells and is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. Moreover, TAF3, along with TRF3, forms a complex that is essential for myogenic differentiation. TAF3 contains a plant homeodomain (PHD) finger. This family also includes Drosophila melanogaster BIP2 (Bric-a-brac interacting protein 2) protein, which functions as an interacting partner of D. melanogaster p53 (Dmp53).

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 405113028 867 ICPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKC 912
Cdd:cd15522    1 ICPICKKPDDGSPMIGCDECDDWYHWECVGITDEPPEEDDWFCPKC 46

Bromodomain associated; This domain is predicted to bind DNA and is often found associated with pfam00439 and in transcription factors. It has a histone-like fold.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 405113028    5 YSRSLLRVSVAQICQALGWDSVQLSACHLLTDVLQRYLQQLGRGCHRYSELYGRTDPILDDVGEAFQLMGVNLHE 79
Cdd:pfam07524   3 LAHDLLKVAVSQILEHAGFDSAEESALETLTDIAQSYIRELGEQAKSFAEHAGRSEPTLFDVVLTLVEMGINVGE 77

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 405113028  867 ICPGCNKPDDGSPMIGCDDCDDWYHWPCVGI---MAAPPEEmQWFCPKC 912
Cdd:pfam00628   1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPpldPAEIPSG-EWLCPEC 48

MAEBL; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 405113028  556 KDKVREREKEKEAGK---EVKYPWKELMKDEESDPYKFKIKEFEDIDAKVRLKDGIVRREREKHK---DKKKDRERGKRE 629
Cdd:PTZ00121 1308 KKKAEEAKKADEAKKkaeEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKkeeAKKKADAAKKKA 1387

                          90       100       110
                  ....*....|....*....|....*....|...
gi 405113028  630 KDKRERERLKEKSREDKIKAPPtqlvLPPKEMA 662
Cdd:PTZ00121 1388 EEKKKADEAKKKAEEDKKKADE----LKKAAAA 1416

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 405113028  554 KEKDKVREREKEKEAGKEVKypwKELMKDEESDPYKFKIKEFEdidakvRLKDGIVRREREKHKDKKKDRERGKREKDKR 633
Cdd:TIGR01622  21 RRRDKGRERSRDRSRDRERS---RSRRRDRHRDRDYYRGRERR------SRSRRPNRRYRPREKRRRRGDSYRRRRDDRR 91

                          90
                  ....*....|....*....
gi 405113028  634 E-RERLKEKSREDKIKAPP 651
Cdd:TIGR01622  92 SrREKPRARDGTPEPLTED 110

Nuclear speckle splicing regulatory protein 1, RS-like domain; This domain found at the C-terminal of Nuclear speckle splicing regulatory protein 1 (NRP1, also known as Nuclear speckle-related protein 70 and Coiled-coil domain-containing protein 55). This is the RS-like domain, that resembles the arginine/serine-rich (RS) domain in other SR proteins, interacts with two SR proteins and with target mRNA, being essential for NRP1 activity. NRP1 is a RNA-binding protein that mediates pre-mRNA alternative splicing regulation.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 405113028  555 EKDKVR---EREKEKEAGKEVKYPWKELMKDEESDPYKfKIKEFEDIDAKVRLKDGIV--RREREKHKDKKKDRERGKRE 629
Cdd:pfam20427  69 QEDKLRgrdQRERNDREWKREKYSSREQERDRQRNDHD-RHSEKGEKEEKSKEKEEHMkgRKERYENSDKYRDREKQEVS 147

                          90
                  ....*....|...
gi 405113028  630 KDKRERERLKEKS 642
Cdd:pfam20427 148 VQSSERNRDRKES 160

PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, transcription initiation factor TFIID 140 kDa subunit (TAF140), or TAFII-140, is an integral component of TFIID) is a general initiation factor (GTF) that plays a key role in preinitiation complex (PIC) assembly through core promoter recognition. The interaction of H3K4me3 with TAF3 directs global TFIID recruitment to active genes, which regulates gene-selective functions of p53 in response to genotoxic stress. TAF3 is highly enriched in embryonic stem cells and is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. Moreover, TAF3, along with TRF3, forms a complex that is essential for myogenic differentiation. TAF3 contains a plant homeodomain (PHD) finger. This family also includes Drosophila melanogaster BIP2 (Bric-a-brac interacting protein 2) protein, which functions as an interacting partner of D. melanogaster p53 (Dmp53).

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 405113028 867 ICPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKC 912
Cdd:cd15522    1 ICPICKKPDDGSPMIGCDECDDWYHWECVGITDEPPEEDDWFCPKC 46

histone-fold domain found in transcription initiation factor TFIID subunit 8 (TAF8) and similar proteins; TAF8, also called TATA Binding Protein (TBP) associated factor 8, protein taube nuss, TBP-associated factor 43 kDa, TBP-associated factor 8, or transcription initiation factor TFIID 43 kDa subunit (TAFII-43, TAFII43), is a component of the TFIID complex that is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). TFIID is one of the general transcription factors required for accurate and regulated initiation by RNA polymerase II. It plays a central role in mediating promoter responses to various activators and repressors. TAF8 mediates both basal and activator-dependent transcription. It is involved in the differentiation of preadipocyte fibroblasts to adipocytes, however, it does not seem to play a role in differentiation of myoblasts. TAF8 is required for the integration of TAF10 in the TAF complex. It may be important for survival of cells of the inner cell mass which constitute the pluripotent cell population of the early embryo.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 405113028   7 RSLLRVSVAQICQALGWDSVQLSACHLLTDVLQRYLQQLGRGCHRYSELYGRTDPILDDVGEAFQLMGVNLHELEDYI 84
Cdd:cd22918    3 RRVLQVAVAALCLEAGFESAEKSALETLTEMLQSYLTEIGRSSKAYCELAGRTEPTLSDVVLALIDMGINVDSLPEYA 80

histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally conserved interaction motif involved in heterodimerization of the core histones and their assembly into the nucleosome octamer. Histone fold heterodimers play crucial roles in gene regulation. The minimal HFD consists of three alpha helices connected by two short, unstructured loops. The HFD is found in core histones, TATA box-binding protein-associated factors (TAFs), and many other transcription factors. HFD plays a role in the nucleosomal core particle by conserving histone interactions; these contain more than one HFD. The structure of the nucleosome core particle has two modes that have the largest interaction surfaces, and these are the H3-H4 and H2A-H2B heterodimer interactions. Several TAFs interact via histone-fold (HF) motifs. Five HF-containing TAF pairs have been described in transcription factor II D (TFIID): TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 405113028   9 LLRVSVAQICQALGWDSVQLSACHLLTDVLQRYLQQLGRGCHRYSELYGRTDPILDDVGEAFQ 71
Cdd:cd00076    1 LLRSAVARILKSAGFDSVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELALE 63

PHD finger found in Set1 complex component SPP1; Set1C component SPP1, also called COMPASS component Spp1, or Complex proteins associated with set1 protein Spp1, or Suppressor of PRP protein 1, is a component of the COMPASS complex that links histone methylation to initiation of meiotic recombination. It induces double-strand break (DSB) formation by tethering to recombinationally cold regions. SPP1 interacts with H3K4me3 and Mer2, a protein required for DSB formation, to promote recruitment of potential meiotic DSB sites to the chromosomal axis. SPP1 contains a PHD finger, a zinc binding motif.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 405113028 871 CNKPDDGSPMIGCDDCDDWYHWPCVGIMAAPPEEM-QWFCPKC 912
Cdd:cd16039    4 CQKPDDGRWMIACDGCDEWYHFTCVNIPEADVELVdSFFCPPC 46

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 405113028 867 ICPGCNKP-DDGSPMIGCDDCDDWYHWPCVGI-MAAPPEEMQWFCPKC 912
Cdd:cd15489    1 SCIVCGKGgDLGGELLQCDGCGKWFHADCLGPpLSSFVPNGKWICPVC 48

PHD finger found in PHD finger protein 3 (PHF3), and death-inducer obliterator variants Dido1, Dido2, and Dido3; PHF3 is a human homolog of yeast protein bypass of Ess1 (Bye1), a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. PHF3 contains an N-terminal plant homeodomain (PHD) finger, a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain. This family also includes Dido gene encoding three alternative splicing variants (Dido1, 2, and 3), which have been implicated in a number of cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. Dido1 is important for maintaining embryonic stem (ES) cells and directly regulates the expression of pluripotency factors. It is the shortest isoform that contains only a highly conserved PHD finger responsible for the binding of histone H3 with a higher affinity for trimethylated lysine4 (H3K4me3). Gene Dido1 is a Bone morphogenetic protein (BMP) target gene and promotes BMP-induced melanoma progression. It also triggers apoptosis after nuclear translocation and caspase upregulation. Dido3 is the largest isoform and is ubiquitously expressed in all human tissues. It is dispensable for ES cell self-renewal and pluripotency, but is involved in the maintenance of stem cell genomic stability and tumorigenesis. Dido3 contains a PHD finger, a transcription elongation factor S-II subunit M (TFSIIM) domain, a SPOC module, and a long C-terminal region (CT) of unknown homology.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 405113028 870 GCNKPDDGSPMIGCDDCDDWYHWPCVGIMAAPPEEM-----QWFCPKC 912
Cdd:cd15552    3 ICRKPHNNRFMICCDRCEEWFHGDCVGITEAQGKEMeenieEYVCPKC 50

PHD finger found in CXXC-type zinc finger protein 1 (Cfp1); Cfp1, also termed CpG-binding protein, or PHD finger and CXXC domain-containing protein 1 (PCCX1), is a specificity factor that binds to unmethylated CpGs and links H3K4me3 with CpG islands (CGIs). It integrates both promoter CpG content and gene activity for accurate trimethylation of histone H3 Lys 4 (H3K4me3) deposition in embryonic stem cells. Moreover, Cfp1 is an essential component of the SETD1 histone H3K4 methyltransferase complex and functions as a critical regulator of histone methylation, cytosine methylation, cellular differentiation, and vertebrate development. Cfp1 contains a plant homeodomain (PHD) finger, a CXXC domain, and a CpG binding protein zinc finger C-terminal domain. Its CXXC domain selectively binds to non-methylated CpG islands, following by a preference for a guanosine nucleotide.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 405113028 871 CNKPDDGSPMIGCDDCDDWYHWPCVGI---MAAPPEEmqWFCPKC 912
Cdd:cd15553    4 CRSSDISRFMIGCDNCEEWYHGDCINItekEAKAIKE--WYCQQC 46

PHD finger found in inhibitor of growth protein 3 (ING3) and similar proteins; ING3, also termed p47ING3, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It is ubiquitously expressed and has been implicated in transcription modulation, cell cycle control, and the induction of apoptosis. It is an important subunit of human NuA4 histone acetyltransferase complex, which regulates the acetylation of histones H2A and H4. Moreover, ING3 promotes ultraviolet (UV)-induced apoptosis through the Fas/caspase-8-dependent pathway in melanoma cells. It physically interacts with subunits of E3 ligase Skp1-Cullin-F-boxprotein complex (SCF complex) and is degraded by the SCF (F-box protein S-phase kinase-associated protein 2, Skp2)-mediated ubiquitin-proteasome system. It also acts as a suppression factor during tumorigenesis and progression of hepatocellular carcinoma (HCC). ING3 contains an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 405113028 871 CNKPDDGSpMIGCDDCD---DWYHWPCVGIMAAPpeEMQWFCPKC 912
Cdd:cd15585    4 CNQVSYGE-MVGCDNDDcpiEWFHYGCVGLTEAP--KGKWYCPQC 45

Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 405113028 871 CNKPDDGsPMIGCD--DCD-DWYHWPCVGIMAAPpeEMQWFCPKC 912
Cdd:COG5034  226 CQQVSYG-QMVACDnaNCKrEWFHLECVGLKEPP--KGKWYCPEC 267

PHD finger found in Arabidopsis thaliana PHD finger protein MALE MEIOCYTE DEATH 1 (MMD1), PHD finger protein MALE STERILITY 1 (MS1), and similar proteins; MMD1 is a plant homeodomain (PHD) finger protein expressed in male meiocytes. It is encoded by the gene DUET, which is required for male meiotic chromosome organization and progression. MMD1 has been implicated in the regulation of gene expression during meiosis. The mmd1 mutation triggers cell death in male meiocytes. MS1 is a nuclear transcriptional activator that is important for tapetal development and pollen wall biosynthesis. It contains a Leu zipper-like domain and a PHD finger motif, both of which are essential for its function.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 405113028 868 CPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKC 912
Cdd:cd15556    2 CSCGTRDDDGERMIACDVCEVWQHTRCVGIADNEEPPDHFLCRRC 46

PHD finger found in plant Alfin1-like (AL) proteins; AL proteins are ubiquitously expressed nuclear proteins existing only in plants. They are involved in chromatin regulation by binding to tri- and dimethylated histone H3 at lysine 4 (H3K4me3/2), the active histone markers, through their plant homeodomain (PHD) fingers.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 405113028 868 CPGCNKP-DDGSPMIGCDDCDDWYHWPCVGIMAAPPEEM-QWFCPKCAN 914
Cdd:cd15613    2 CGSCGGNyTADEFWICCDVCEKWYHGKCVKITPAKAEHIkQYKCPSCSN 50

PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 405113028 868 CPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMAAPpeEMQWFCPKC 912
Cdd:cd15529    2 CTKCGDPHDEDKMMFCDQCDRGYHTFCVGLRSIP--DGRWICPLC 44

PHD finger found in inhibitor of growth protein 4 (ING4) and 5 (ING5); ING4, also termed p29ING4, and ING5, also termed p28ING5, belong to the inhibitor of growth (ING) family of type II tumor suppressors. ING4 acts as an E3 ubiquitin ligase to induce ubiquitination of the p65 subunit of NF-kappaB and inhibit the transactivation of NF-kappaB target genes. It also induces apoptosis through a p53 dependent pathway, including increasing p53 acetylation, inhibiting Mdm2-mediated degradation of p53 and enhancing the expression of p53 responsive genes both at the transcriptional and post-translational levels. Moreover, ING4 can inhibit the translation of proto-oncogene MYC by interacting with AUF1. It also regulates other transcription factors, such as hypoxia-inducible factor (HIF). ING5 is a Tip60 cofactor that acetylates p53 at K120 and subsequently activates the expression of p53-dependent apoptotic genes in response to DNA damage. Aberrant ING5 expression may contribute to pathogenesis, growth, and invasion of gastric carcinomas and colorectal cancer. ING5 can physically interact with p300 and p53 in vivo, and its overexpression induces apoptosis in colorectal cancer cells. It also associates with cyclin A1 (INCA1) and functions as a growth suppressor with suppressed expression in Acute Myeloid Leukemia (AML). Moreover, ING5 translocation from the nucleus to the cytoplasm might be a critical event for carcinogenesis and tumor progression in human head and neck squamous cell carcinoma. Both ING4 and ING5 contain an N-terminal ING histone-binding domain and a C-terminal plant homeodomain (PHD) finger. They associate with histone acetyltransferase (HAT) complexes containing MOZ (monocytic leukemia zinc finger protein)/MORF (MOZ-related factor) and HBO1, and further direct the MOZ/MORF and HBO1 complexes to chromatin.

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 405113028 880 MIGCDDCD---DWYHWPCVGIMAAPpeEMQWFCPKC 912
Cdd:cd15586   12 MIGCDNPDcpiEWFHFACVGLTTKP--KGKWFCPRC 45

PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins; Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model corresponds to the first PHD finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 405113028 868 CPGCNKPDDGSPMIGCDDCDDWYHWPCVG--IMAAPPEEmqWFCPKC 912
Cdd:cd15519    2 CEVCGLDDNEGEVLLCDGCDAEYHTSCLDppLGEIPPGT--WFCPSC 46

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 405113028 868 CPGCNKPDDGSPMIGCDDCDDWYHWPCVG-IMAAPPEEMQWFCPKC 912
Cdd:cd15525    2 CHVCGGKQDPEKQLLCDECDMAYHLYCLDpPLTSLPDDDEWYCPDC 47

PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar proteins. PHF2, also termed GRC5, or PHD finger protein 2, is a histone lysine demethylase ubiquitously expressed in various tissues. PHF8, also termed PHD finger protein 8, or KDM7B, is a monomethylated histone H4 lysine 20(H4K20me1) demethylase that transcriptionally regulates many cell cycle genes. It also preferentially acts on H3K9me2 and H3K9me1. PHF8 is modulated by CDC20-containing anaphase-promoting complex (APC (cdc20)) and plays an important role in the G2/M transition. It acts as a critical molecular sensor for mediating retinoic acid (RA) treatment response in RAR alpha-fusion-induced leukemia. Moreover, PHF8 is essential for cytoskeleton dynamics and is associated with X-linked mental retardation. KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. All family members contain a plant homeodomain (PHD) finger and a JmjC domain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 405113028 871 CNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWF-CPKC 912
Cdd:cd15554    4 CRQPYDvTRFMIECDVCKDWFHGSCVGVEEHQANDIERYhCPNC 47

PHD finger found in death-inducer obliterator variants Dido1, Dido2, and Dido3; This family includes three alternative splicing variants (Dido1, 2, and 3) encoded by the Dido gene, which have been implicated in a number of cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. Dido1, also termed DIO-1, or death-associated transcription factor 1 (DATF-1), is important for maintaining embryonic stem (ES) cells and directly regulates the expression of pluripotency factors. It is the shortest isoform that contains only a highly conserved plant homeodomain (PHD) finger responsible for the binding of histone H3 with a higher affinity for trimethylated lysine 4 (H3K4me3). Gene Dido is a Bonemorphogenetic protein (BMP) target gene, which promotes BMP-induced melanoma progression. It also triggers apoptosis after nuclear translocation and caspase upregulation. Dido3 is the largest isoform ubiquitously expressed in all human tissues. It is dispensable for ES cell self-renewal and pluripotency, but involved in the maintenance of stem cell genomic stability and tumorigenesis. Dido3 contains a PHD finger, a transcription elongation factor S-II subunit M (TFSIIM) domain, aspen paralog and ortholog (SPOC) module, and a long C-terminal region (CT) of unknown homology. Its PHD finger interacts with H3K4me3.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 405113028 871 CNKPDDGSPMIGCDDCDDWYHWPCVGIMAAPPEEMQ-----WFCPKC 912
Cdd:cd15639    8 CRQPHNNRFMICCDRCEEWFHGDCVGITEARGRLLErngedYICPNC 54

PHD finger found in protein Jade-1 and similar proteins; Jade-1, also termed PHD finger protein 17 (PHF17), is a novel binding partner of von Hippel-Lindau (VHL) tumor suppressor Pvhl, a key regulator of the cellular oxygen sensing pathway. It is highly expressed in renal proximal tubules. Jade-1 functions as an essential regulator of multiple cell signaling pathways. It may be involved in the serine/threonine kinase AKT/AKT1 pathway during renal cancer pathogenesis and normally prevents renal epithelial cell proliferation and transformation. It also acts as a pro-apoptotic and growth suppressive ubiquitin ligase to inhibit canonical Wnt downstream effector beta-catenin for proteasomal degradation, and as a transcription factor associated with histone acetyltransferase activity and with increased abundance of cyclin-dependent kinase inhibitor p21. Moreover, Jade-1 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex, and plays a role in epithelial cell regeneration. It has also been identified as a novel component of the nephrocystin protein (NPHP) complex and interacts with the ciliary protein nephrocystin-4 (NPHP4). Jade-1 contains a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 405113028 867 ICPGCNKPD--DGSPMIGCDDCDDWYHWPCVGIMAAPpeEMQWFCPKC 912
Cdd:cd15679    1 VCDVCQSPDgeDGNEMVFCDKCNICVHQACYGILKVP--EGSWLCRTC 46

PHD finger found in inhibitor of growth protein 1 (ING1) and 2 (ING2); ING1 is an epigenetic regulator and a type II tumor suppressor that impacts cell growth, aging, apoptosis, and DNA repair, by affecting chromatin conformation and gene expression. It acts as a reader of the active chromatin mark, the trimethylation of histone H3 lysine 4 (H3K4me3). It binds and directs Growth arrest and DNA damage inducible protein 45 a (Gadd45a) to target sites, thus linking the histone code with DNA demethylation. It interacts with the proliferating cell nuclear antigen (PCNA) via the PCNA-interacting protein (PIP) domain in a UV-inducible manner. It also interacts with a PCNA-interacting protein, p15 (PAF). Moreover, ING1 associates with members of the 14-3-3 family, which is necessary for cytoplasmic relocalization. Endogenous ING1 protein specifically interacts with the pro-apoptotic BCL2 family member BAX and colocalizes with BAX in a UV-inducible manner. It stabilizes the p53 tumor suppressor by inhibiting polyubiquitination of multi-monoubiquitinated forms via interaction with and colocalization of the herpesvirus-associated ubiquitin-specific protease (HAUSP)-deubiquitinase with p53. It is also involved in trichostatin A-induced apoptosis and caspase 3 signaling in p53-deficient glioblastoma cells. In addition, tyrosine kinase Src can bind and phosphorylate ING1 and further regulates its activity. ING2, also termed inhibitor of growth 1-like protein (ING1Lp), or p32, or p33ING2, belongs to the inhibitor of growth (ING) family of type II tumor suppressors. It is a core component of a multi-factor chromatin-modifying complex containing the transcriptional co-repressor SIN3A and histone deacetylase 1 (HDAC1). It has been implicated in the control of cell cycle, in genome stability, and in muscle differentiation. ING2 independently interacts with H3K4me3 (Histone H3 trimethylated on lysine 4) and PtdIns(5)P, and modulates crosstalk between lysine methylation and lysine acetylation on histone proteins through association with chromatin in the presence of DNA damage. It collaborates with SnoN to mediate transforming growth factor (TGF)-beta-induced Smad-dependent transcription and cellular responses. It is upregulated in colon cancer and increases invasion by enhanced MMP13 expression. It also acts as a cofactor of p300 for p53 acetylation and plays a positive regulatory role during p53-mediated replicative senescence. Both ING1 and ING2 contain an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 405113028 871 CNKPDDGSpMIGCDD--CD-DWYHWPCVGIMAAPpeEMQWFCPKC 912
Cdd:cd15584    4 CNQVSYGE-MIGCDNdeCPiEWFHFSCVGLTHKP--KGKWYCPKC 45

PHD finger found in protein Jade-3 and similar proteins; Jade-3, also termed PHD finger protein 16 (PHF16), is a plant homeodomain (PHD) zinc finger protein that is closely related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-3 is required for ING4 and ING5 to associate with histone acetyl transferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-3 contains a canonical Cys4HisCys3 PHD domain followed by a non-canonical extended PHD (ePHD) domain, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 405113028 867 ICPGCNKPD--DGSPMIGCDDCDDWYHWPCVGIMAAPpeEMQWFCPKC 912
Cdd:cd15681    1 ICDVCRSPDseEGNDMVFCDKCNICVHQACYGILKVP--EGSWLCRTC 46

PHD finger found in lysine-specific demethylase 7 (KDM7); KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. KDM7 contains a plant homeodomain (PHD) that binds Lys4-trimethylated histone 3 (H3K4me3) and a jumonji domain that demethylates either H3K9me2 or H3K27me2.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 405113028 871 CNKPDDGSP-MIGCDDCDDWYHWPCVGIMAAPPEEMQWF-CPKCA 913
Cdd:cd15640    4 CRQPYDVNRfMIECDICKDWFHGSCVQVEEHHAADIDLYhCPNCE 48

PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also termed KIAA1542, or CTD-binding SR-like protein rA9, is a ubiquitin ligase that induces the ubiquitination of TGIF (TG-interacting factor) at lysine 130. It acts as a tumor suppressor that promotes the transforming growth factor (TGF)-beta cytostatic program through selective release of TGIF-driven promyelocytic leukemia protein (PML) inactivation. PHRF1 contains a plant homeodomain (PHD) finger and a RING finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 405113028 868 CPGCNKPDDGSPMIGCDDCDDWYHWPCVG--IMAAPPEEmqWFCPKC 912
Cdd:cd15536    2 CEVCGRSDREDRLLLCDGCDAGYHMECLTppLDEVPIEE--WFCPEC 46

PHD domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p), the E3 Sumo Ligase SIZ1, and similar proteins; Yeast Bye1p is a nuclear transcription factor with a domain resembling the central domain in the transcription elongation factor TFIIS and plays an inhibitory role during transcription elongation. It functions as a multicopy suppressor of Ess1, a peptidyl-prolyl cis-trans isomerase involved in proline isomerization of the C-terminal domain (CTD) of RNA polymerase II (Pol II). Bye1p contains an N-terminal plant homeodomain (PHD) finger, a central Pol II-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain. The PHD domain binds to a histone H3 tail peptide containing trimethylated lysine 4 (H3K4me3). The TLD domain is responsible for the association with chromatin. Plant SIZ1 protein is a SUMO (small ubiquitin-related modifier) E3 ligase that facilitates conjugation of SUMO to substrate target proteins (sumoylation) and belongs to the protein inhibitor of activated STAT (PIAS) protein family. It negatively regulates abscisic acid (ABA) signaling, which is dependent on the bZIP transcripton factor ABI5. It also modulates plant growth and plays a role in drought stress response likely through the regulation of gene expression. SIZ1 functions as a floral repressor that not only represses the salicylic acid (SA)-dependent pathway, but also promotes FLOWERING LOCUS C (FLC) expression by repressing FLOWERING LOCUS D (FLD) activity through sumoylation. SIZ1 contains a PHD finger, which specifically binds methylated histone H3 at lysine 4 and arginine 2.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 405113028 868 CPgCNKPDDGSPMIGCDDCDDWYHWPCVGI----MAAPPEE-MQWFCPKC 912
Cdd:cd15570    2 CP-CGSSMEDGSMIQCEGCKTWQHMDCVLIpdkpADGLPELpSKFYCELC 50

PHD finger found in proteins Jade-1, Jade-2, Jade-3, and similar proteins; This family includes proteins Jade-1 (PHF17), Jade-2 (PHF15), and Jade-3 (PHF16), each of which is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. This family also contains Drosophila melanogaster PHD finger protein rhinoceros (RNO). It is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating transcription of key EGFR/Ras pathway regulators in the Drosophila eye. All Jade proteins contain a canonical Cys4HisCys3 PHD finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 405113028 867 ICPGCNKPD--DGSPMIGCDDCDDWYHWPCVGIMAAPpeEMQWFCPKC 912
Cdd:cd15573    1 VCDVCRSPDseEGNEMVFCDKCNICVHQACYGIQKIP--EGSWLCRTC 46

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B (BAZ2B); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A. Both BAZ2A and BAZ2B contain a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain. BAZ2B also harbors an extra Apolipophorin-III like domain in its N-terminal region.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 405113028 868 CPGCNKPDDGSPMIGCDDCDDWYHWPCVGI-MAAPPEEmQWFCPKC 912
Cdd:cd15545    2 CQICRSGDNEDQLLLCDGCDRGYHTYCFKPkMTNVPEG-DWFCPEC 46

PHD finger found in protein Jade-2 and similar proteins; Jade-2, also termed PHD finger protein 15 (PHF15), is a plant homeodomain (PHD) zinc finger protein that is closely related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-2 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-2 contains a canonical Cys4HisCys3 PHD finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 405113028 867 ICPGCNKPD--DGSPMIGCDDCDDWYHWPCVGIMAAPpeEMQWFCPKC 912
Cdd:cd15680    1 VCDVCRSPEgeDGNEMVFCDKCNVCVHQACYGILKVP--TGSWLCRTC 46

PHD finger found in PHD finger proteins PHF13 and PHF23; PHF13, also termed survival time-associated PHD finger protein in ovarian cancer 1 (SPOC1), is a novel plant homeodomain (PHD) finger-containing protein that shows strong expression in spermatogonia and ovarian cancer cells, modulates chromatin structure and mitotic chromosome condensation, and is important for proper cell division. It is also required for spermatogonial stem cell differentiation and sustained spermatogenesis. The overexpression of PHF13 associates with unresectable carcinomas and shorter survival in ovarian cancer. PHF23, also termed PHD-containing protein JUNE-1, is a hypothetical protein with a PHD finger. It is encoded by gene PHF23 that acts as a candidate fusion partner for the nucleoporin gene NUP98. The NUP98-PHF23 fusion results from a cryptic translocation t(11;17)(p15;p13) in acute myeloid leukemia (AML).

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 405113028 871 CNKPDDGSPMIGCDDCDDWYHWPCVGIMAAP-PEEmqWFCPKC 912
Cdd:cd15546    4 CGKPFAGRPMIECSECLTWIHLSCAKIRKNNvPEV--FICQKC 44

PHD finger found in inhibitor of growth protein 2 (ING2); ING2, also termed inhibitor of growth 1-like protein (ING1Lp), or p32, or p33ING2, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It is a core component of a multi-factor chromatin-modifying complex containing the transcriptional co-repressor SIN3A and histone deacetylase 1 (HDAC1). It has been implicated in the control of cell cycle, in genome stability, and in muscle differentiation. ING2 independently interacts with H3K4me3 (Histone H3 trimethylated on lysine 4) and PtdIns(5)P, and modulates crosstalk between lysine methylation and lysine acetylation on histone proteins through association with chromatin in the presence of DNA damage. It collaborates with SnoN to mediate transforming growth factor (TGF)-beta-induced Smad-dependent transcription and cellular responses. It is upregulated in colon cancer and increases invasion by enhanced MMP13 expression. It also acts as a cofactor of p300 for p53 acetylation and plays a positive regulatory role during p53-mediated replicative senescence. ING2 contains an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 405113028 871 CNKPDDGSpMIGCDD--CD-DWYHWPCVGIMAAPpeEMQWFCPKC 912
Cdd:cd15683    5 CNQVSYGE-MIGCDNeqCPiEWFHFSCVGLTYKP--KGKWYCPKC 46

PHD finger found in Arabidopsis thaliana AT-rich interactive domain-containing protein 4 (ARID4) and similar proteins; This family includes A. thaliana ARID4 (ARID domain-containing protein 4) and similar proteins. Their biological roles remain unclear, but they all contain an AT-rich interactive domain (ARID) and a plant homeodomain (PHD) finger at the C-terminus. ARID is a helix-turn-helix motif-based DNA-binding domain conserved in all eukaryotes. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 405113028 868 CPGCNK-----PDDGSPMIGCDDCDDWYHWPCVGI------MAAPPEEMQWFCPKC 912
Cdd:cd15615    2 CILCGQvyeenEGDEKEWVQCDSCSEWVHFECDGRtglgafKYAKSDGLQYVCPRC 57

PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; The family includes BRPF proteins, Jade proteins, protein AF-10 and AF-17. BRPF proteins are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. Jade proteins are required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6, to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. AF-10, also termed ALL1 (acute lymphoblastic leukemia)-fused gene from chromosome 10 protein, is a transcription factor that has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is a putative transcription factor that may play a role in multiple signaling pathways. All Jade proteins, AF-10, and AF-17 contain a canonical PHD finger followed by a non-canonical ePHD finger. This model corresponds to the canonical PHD finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 405113028 871 CNKPD--DGSPMIGCDDCDDWYHWPCVGIMAAPpeEMQWFCPKC 912
Cdd:cd15492    5 CLDGEseDDNEIVFCDGCNVAVHQSCYGIPLIP--EGDWFCRKC 46

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 405113028  235 DSTDLAPPSPEPPMLAPFAKSQLPIAKPLETKPFTP-KTKTKASSPGQKTKSPKAALSPARLGSPIRSPKTIPKEKKSPG 313
Cdd:pfam05109 426 ESTTTSPTLNTTGFAAPNTTTGLPSSTHVPTNLTAPaSTGPTVSTADVTSPTPAGTTSGASPVTPSPSPRDNGTESKAPD 505

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 405113028  314 RSKSPKSPKSPKIVTHVPQPPVRPETPNRT--------PSAMVVEKTVKETIPVKPTQTP-PETGKLNIEMQLKKGVVTD 384
Cdd:pfam05109 506 MTSPTSAVTTPTPNATSPTPAVTTPTPNATsptlgktsPTSAVTTPTPNATSPTPAVTTPtPNATIPTLGKTSPTSAVTT 585

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 405113028  385 KTIDDSIDAViaracAEREP--DPFEFSSGSESEGDTFTSPKRISVSECTTPKASTSSNNFTKSLATPLPLSG--GTSSS 460
Cdd:pfam05109 586 PTPNATSPTV-----GETSPqaNTTNHTLGGTSSTPVVTSPPKNATSAVTTGQHNITSSSTSSMSLRPSSISEtlSPSTS 660

                  ...
gi 405113028  461 DNS 463
Cdd:pfam05109 661 DNS 663